R Notebook

pacman::p_load(tidyverse, corrr, ggplot2, lmerTest, ggeffects, sjPlot, tidyverse, heatmaply, pheatmap, gplots, RColorBrewer)

setwd("/Volumes/GoogleDrive/My Drive/Volumes/Research Project/Preference Falsification/Analysis/")

Warning: The working directory was changed to /Volumes/GoogleDrive/My Drive/Volumes/Research Project/Preference Falsification/Analysis inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.

indDiffDf <- read.csv("./output/PFindDiffDf.csv")
indDiffDf[c("Rep","Info", "partyN")] <- NULL
#longDf <- read.csv("./output/PFfullDf.csv")
longDf <- read.csv("./output/PFfullDfzip.csv")
indDiffDf <- merge(indDiffDf, longDf[match(unique(longDf$subID), longDf$subID),][c("subID","Polit")], by = "subID")
indDiffDf$polStrength <- abs(7- indDiffDf$Polit )
issExpDf <- read.csv("./output/issueAgDf.csv")
longDf$partyN <- as.factor(longDf$partyN)
longDf$Rep <- as.factor(longDf$Rep)
contrasts(longDf$Rep) <- contr.sum(3)
longDf$RepN <- as.factor(longDf$RepN)
longDf$RepN <- relevel(longDf$RepN,"In")
longDf$Info <- as.factor(longDf$Info)
contrasts(longDf$Info) <- contr.sum(2)
longDf$partyN <- as.factor(longDf$partyN)
contrasts(longDf$partyN) <- contr.sum(2)
longDf <- longDf[order(longDf$subID, longDf$issues),]
demDf <- subset(longDf, partyN == "Dem")
repDf <- subset(longDf, partyN == "Rep")
shortDf1 <- longDf[!duplicated(longDf$subID),]

longDfc<- longDf[c("subID","issues","eval")]
longDfc <- longDfc[order(longDfc$subID, longDfc$issues),]
wideDf <- longDfc %>% pivot_wider(names_from = issues, values_from = eval)

corMat <- wideDf %>% select(`1`:`100`) %>% cor(.,use="pairwise.complete.obs")
corMatZ <- psych::fisherz(corMat)
corVector <- corMatZ[lower.tri(corMatZ)]

colnames(corMat) <- longDf$label[match(unique(longDf$issues), longDf$issues) ]
rownames(corMat) <- longDf$label[match(unique(longDf$issues), longDf$issues) ]
jpeg("~/Desktop/test.png", height=10, width=15, units="in",res=300)
heatmap(corMat, Colv = "Rowv", symm=TRUE, cexRow=.5, cexCol=.5)
dev.off()

null device 
          1 

jpeg("~/Desktop/test.png", height=12, width=30, units="in",res=300)
outphm<-pheatmap(corMat, fontsize_row = 6, fontsize_col = 6, angle_col = 45, angle_row =45, width=100, height = 200 )
outphm

dev.off()

null device 
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outphm

out<-heatmaply::ggheatmap(corMat, grid_gap=2, colorbar_len=50, grid_size = 5 , Rowv=outphm[[1]], Colv=outphm[[2]], revC=TRUE, fontsize_row = 8.5, fontsize_col = 8.5, angle_col = 45, angle_row =45,  limits = c(-1, 1), colors = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100))

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

jpeg("~/Desktop/test.png", height=15, width=20, units="in",res=300)
out

dev.off()

quartz_off_screen 
                2 

library(RColorBrewer)
out<-heatmaply::ggheatmap(corMat, colorbar_len=50, grid_size = 5 , Rowv=outphm[[1]], Colv=outphm[[2]], revC=TRUE, fontsize_row = 8.5, fontsize_col = 8.5, angle_col = 45, angle_row =45,  limits = c(-1, 1), colors = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100))

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

out
ggsave("~/Desktop/test2.png", dpi=300,units="in",height=20,width=20)

heatmaply_cor(round(corMat,3), Rowv=outphm[[1]], Colv=outphm[[2]], revC=TRUE, fontsize_row = 2.5, fontsize_col = 2.5, angle_col = 45, angle_row =45,  limits = c(-1, 1), colors = colorRampPalette(rev(brewer.pal(n = 7, name =
  "RdYlBu")))(100) )

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

mds2<-corMat %>%
  psych::cor2dist(.) %>%
  MASS::isoMDS(k=2) %>%
  .$points %>%
  as_tibble()

initial  value 16.681209 
iter   5 value 12.639758
iter  10 value 12.193377
final  value 12.166250 
converged

Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Using compatibility `.name_repair`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

colnames(mds2) <- c("Dim.1", "Dim.2")
library(ggpubr)

Registered S3 methods overwritten by 'car':
  method                          from
  influence.merMod                lme4
  cooks.distance.influence.merMod lme4
  dfbeta.influence.merMod         lme4
  dfbetas.influence.merMod        lme4

ggscatter(mds2, x = "Dim.1", y = "Dim.2", 
          label = longDf$label[match(unique(longDf$issues), longDf$issues) ],
          font.label = c(5, "bold", "black"),
          size = 1,
          repel = TRUE)

allDists <- tapply(longDf$eval, longDf$subID, dist)

issuesFrame <- longDf[match(unique(longDf$issues), 1:100),]

allDistsOut <- tapply(longDf$bootEvalOut, longDf$subID, dist)

allDistsIn <- tapply(longDf$bootEvalIn, longDf$subID, dist)

demIssues <- demDf[match(unique(demDf$issues), 1:100),]
repIssues <- repDf[match(unique(repDf$issues), 1:100),]

demDistM<-as.matrix(dist(c(demIssues$bootEvalIn, demIssues$bootEvalOut)))
demDistM<-as.matrix(demDistM[-(1:100),-(101:200)])
demDistV <- demDistM[lower.tri(demDistM)]

repDistM<-as.matrix(dist(c(repIssues$bootEvalIn, repIssues$bootEvalOut)))
repDistM<-as.matrix(repDistM[-(1:100),-(101:200)])
repDistV <- repDistM[lower.tri(repDistM)]

reputDist <- dist(issuesFrame$reput)
reputMatrix <- as.matrix(reputDist)
reputVector <- reputMatrix[lower.tri(reputMatrix)]

reputDDist <- dist(issuesFrame$reputD)
reputDMatrix <- as.matrix(reputDDist)
reputDVector <- reputDMatrix[lower.tri(reputDMatrix)]

honestDist <- dist(issuesFrame$honest)
honestMatrix <- as.matrix(honestDist)
honestVector <- honestMatrix[lower.tri(honestMatrix)]

changeDist <- dist(issuesFrame$change)
changeMatrix <- as.matrix(changeDist)
changeVector <- changeMatrix[lower.tri(changeMatrix)]

politicDist <- dist(issuesFrame$politic)
politicMatrix <- as.matrix(politicDist)
politicVector <- politicMatrix[lower.tri(politicMatrix)]

breadthDist <- dist(issuesFrame$breadth)
breadthMatrix <- as.matrix(breadthDist)
breadthVector <- breadthMatrix[lower.tri(breadthMatrix)]

fullMat <- as.data.frame(matrix(ncol=16))
uIds<-unique(longDf$subID)
for(i in 1:length(uIds)){
  j <- uIds[i]
  
  distMatrix <- as.matrix(allDists[[i]])
  distVector <- distMatrix[lower.tri(distMatrix)]
  
  distMatrixOut <- as.matrix(allDistsOut[[i]])
  distVectorOut <- distMatrixOut[lower.tri(distMatrixOut)]
  
  distMatrixIn <- as.matrix(allDistsIn[[i]])
  distVectorIn <- distMatrixOut[lower.tri(distMatrixIn)]
  
  if( as.character(unique(longDf$partyN[longDf$subID==j]))=="Rep" ){
    partyDistV <- repDistV
  }else if( as.character(unique(longDf$partyN[longDf$subID==j]))=="Dem" ){
    partyDistV <- demDistV
  }
  
  subMat <- cbind(data.frame(subID=j,dist=distVector,RepN=unique(longDf$RepN[longDf$subID==j]), partyN=unique(longDf$partyN[longDf$subID==j]), Info=unique(longDf$Info[longDf$subID==j]), Rep=unique(longDf$Rep[longDf$subID==j]), reputD = reputVector, reputDD = reputDVector, changeD = changeVector, honestD = honestVector, politicD = politicVector, breadthD = breadthVector, distOut = distVectorOut, distIn = distVectorIn, distParty  = partyDistV, corr = corVector ))
  names(fullMat) <- colnames(subMat)
  fullMat <- rbind(fullMat, subMat)
}

#x <- c("subID","dist")
#fullDistDf <- as.data.frame(fullMat)
#names(fullDistDf) <- x
fullDistDf <- as.data.frame(fullMat)
fullDistDf<-fullDistDf[!is.na(fullDistDf$subID),]

fullDistDf$distSTrans <- 1/(1+fullDistDf$dist)
fullDistDf$distETrans <- 1/(exp(fullDistDf$dist))

#fullDistDf <- merge(fullDistDf, longDf[c("subID","RepN","partyN","Info")], by = "subID")

fullDistDf <- merge(fullDistDf, indDiffDf, by = "subID")

colnames(fullDistDf)

 [1] "subID"        "dist"         "RepN"         "partyN"       "Info"         "Rep"          "reputD"       "reputDD"     
 [9] "changeD"      "honestD"      "politicD"     "breadthD"     "distOut"      "distIn"       "distParty"    "corr"        
[17] "distSTrans"   "distETrans"   "inTherm"      "outTherm"     "affPol"       "Extra"        "Neur"         "MLAM"        
[25] "SCS.pub"      "SCS.priv"     "SCS.sa"       "WSC"          "NFC"          "SGO.wt"       "SGO.st"       "SGO.sw"      
[33] "CSEpriv"      "CSEpub"       "CSEid"        "falsify"      "bDiffInMean"  "bDiffOutMean" "Polit"        "polStrength" 

fullDistDf <- fullDistDf %>% select(subID, dist, RepN, partyN, Info, Rep, corr, distSTrans, distETrans, affPol:falsify, Polit, polStrength)

write.csv(fullDistDf, "~/Google Drive/Volumes/Research Project/Preference Falsification/Analysis/output/distanceDf.csv")

arrow::write_parquet(fullDistDf, "~/Google Drive/Volumes/Research Project/Preference Falsification/Analysis/output/distanceDf.parquet")

longDf2c<- longDf2[c("subID","issues","eval")]
longDf2c <- longDf2c[order(longDf2c$subID, longDf2c$issues),]
wideDf <- longDf2c %>% pivot_wider(names_from = issues, values_from = eval)

corMat <- wideDf %>% select(`1`:`100`) %>% cor(.,use="pairwise.complete.obs")
corMatZ <- psych::fisherz(corMat)
corVector <- corMatZ[lower.tri(corMatZ)]

colnames(corMat) <- longDf2$label.x[match(unique(longDf2$issues), longDf2$issues) ]
rownames(corMat) <- longDf2$label.x[match(unique(longDf2$issues), longDf2$issues) ]
jpeg("~/Desktop/test.png", height=10, width=15, units="in",res=300)
heatmap(corMat, Colv = "Rowv", symm=TRUE, cexRow=.5, cexCol=.5)
dev.off()

null device 
          1 

jpeg("~/Desktop/test.png", height=12, width=30, units="in",res=300)
outphm<-pheatmap(corMat, fontsize_row = 6, fontsize_col = 6, angle_col = 45, angle_row =45, width=100, height = 200 )
outphm

dev.off()

null device 
          1 

outphm

out<-heatmaply::ggheatmap(corMat, grid_gap=2, colorbar_len=50, grid_size = 5 , Rowv=outphm[[1]], Colv=outphm[[2]], revC=TRUE, fontsize_row = 8.5, fontsize_col = 8.5, angle_col = 45, angle_row =45,  limits = c(-1, 1), colors = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100))

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

jpeg("~/Desktop/test.png", height=15, width=20, units="in",res=300)
out

dev.off()

quartz_off_screen 
                2 

out<-heatmaply::ggheatmap(corMat, colorbar_len=50, grid_size = 5 , Rowv=outphm[[1]], Colv=outphm[[2]], revC=TRUE, fontsize_row = 8.5, fontsize_col = 8.5, angle_col = 45, angle_row =45,  limits = c(-1, 1), colors = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100))

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

out
ggsave("~/Desktop/test2.png", dpi=300,units="in",height=20,width=20)

heatmaply_cor(round(corMat,3), Rowv=outphm[[1]], Colv=outphm[[2]], revC=TRUE, fontsize_row = 2.5, fontsize_col = 2.5, angle_col = 45, angle_row =45,  limits = c(-1, 1), colors = colorRampPalette(rev(brewer.pal(n = 7, name =
  "RdYlBu")))(100) )

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

mds2<-corMat %>%
  psych::cor2dist(.) %>%
  MASS::isoMDS(k=2) %>%
  .$points %>%
  as_tibble()

initial  value 18.781471 
iter   5 value 14.617077
final  value 14.331974 
converged

colnames(mds2) <- c("Dim.1", "Dim.2")
library(ggpubr)
ggscatter(mds2, x = "Dim.1", y = "Dim.2", 
          label = longDf2$label.x[match(unique(longDf2$issues), longDf2$issues) ],
          font.label = c(5, "bold", "black"),
          size = 1,
          repel = TRUE)

write.csv(fullDistDf2, "/Volumes/GoogleDrive/My Drive/Volumes/Research Project/Preference Falsification/Study 2 Analysis/output/distanceDf2.csv")

Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/Volumes/GoogleDrive/My Drive/Volumes/Research Project/Preference Falsification/Study 2 Analysis/output/distanceDf2.csv': Resource temporarily unavailable
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection